1
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Peterson SM, Watowich MM, Renner LM, Martin S, Offenberg E, Lea A, Montague MJ, Higham JP, Snyder-Mackler N, Neuringer M, Ferguson B. Genetic variants in melanogenesis proteins TYRP1 and TYR are associated with the golden rhesus macaque phenotype. G3 (BETHESDA, MD.) 2023; 13:jkad168. [PMID: 37522525 PMCID: PMC10542561 DOI: 10.1093/g3journal/jkad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/09/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Nonhuman primates (NHPs) are vital translational research models due to their high genetic, physiological, and anatomical homology with humans. The "golden" rhesus macaque (Macaca mulatta) phenotype is a naturally occurring, inherited trait with a visually distinct pigmentation pattern resulting in light blonde colored fur. Retinal imaging also reveals consistent hypopigmentation and occasional foveal hypoplasia. Here, we describe the use of genome-wide association in 2 distinct NHP populations to identify candidate variants in genes linked to the golden phenotype. Two missense variants were identified in the Tyrosinase-related protein 1 gene (Asp343Gly and Leu415Pro) that segregate with the phenotype. An additional and distinct association was also found with a Tyrosinase variant (His256Gln), indicating the light-colored fur phenotype can result from multiple genetic mechanisms. The implicated genes are related through their contribution to the melanogenesis pathway. Variants in these 2 genes are known to cause pigmentation phenotypes in other species and to be associated with oculocutaneous albinism in humans. The novel associations presented in this study will permit further investigations into the role these proteins and variants play in the melanogenesis pathway and model the effects of genetic hypopigmentation and altered melanogenesis in a naturally occurring nonhuman primate model.
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Affiliation(s)
- Samuel M Peterson
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Marina M Watowich
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren M Renner
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Samantha Martin
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Emma Offenberg
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Amanda Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James P Higham
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School for Human Evolution & Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Martha Neuringer
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
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2
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Van Zandt AR, MacLean AG. Advances in HIV therapeutics and cure strategies: findings obtained through non-human primate studies. J Neurovirol 2023; 29:389-399. [PMID: 37635184 DOI: 10.1007/s13365-023-01162-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Human immunodeficiency virus (HIV), the main contributor of the ongoing AIDS epidemic, remains one of the most challenging and complex viruses to target and eradicate due to frequent genome mutation and immune evasion. Despite the development of potent antiretroviral therapies, HIV remains an incurable infection as the virus persists in latent reservoirs throughout the body. To innovate a safe and effective cure strategy for HIV in humans, animal models are needed to better understand viral proliferation, disease progression, and therapeutic response. Nonhuman primates infected with simian immunodeficiency virus (SIV) provide an ideal model to study HIV infection and pathogenesis as they are closely related to humans genetically and express phenotypically similar immune systems. Examining the clinical outcomes of novel treatment strategies within nonhuman primates facilitates our understanding of HIV latency and advances the development of a true cure to HIV.
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Affiliation(s)
- Alison R Van Zandt
- Tulane National Primate Research Center, Covington, LA, USA
- Biomedical Sciences Training Program, Tulane University School of Medicine, New Orleans, LA, USA
| | - Andrew G MacLean
- Tulane National Primate Research Center, Covington, LA, USA.
- Biomedical Sciences Training Program, Tulane University School of Medicine, New Orleans, LA, USA.
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
- Tulane Brain Institute, New Orleans, LA, USA.
- Tulane Center for Aging, New Orleans, LA, USA.
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3
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Min F, Xu F, Huang S, Wu R, Zhang L, Wang J. Genetic diversity of Chinese laboratory macaques based on 2b-RAD simplified genome sequencing. J Med Primatol 2022; 51:101-107. [PMID: 35165897 DOI: 10.1111/jmp.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/27/2021] [Accepted: 02/01/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Currently, Chinese laboratory macaques are widely used in biomedical research. Correspondingly, clarity regarding the genetic diversity of Chinese laboratory macaques is important for both vendors and users. METHODS Genome sequences of 55 laboratory macaques (40 cynomolgus macaques and 15 rhesus macaques) bred in South China were analyzed using 2b-RAD simplified genome sequencing. RESULTS A total of 115,681 single-nucleotide polymorphisms (SNPs) were found that were distributed in 21 chromosomes and an unplaced scaffold. Genetic diversity indices varied across populations and exhibited low values. The results of principal coordinate analysis (PCA) were consistent with those of the arithmetic mean (UPGMA) clustered tree and supported the structure analysis, demonstrating that the genetic differentiation in rhesus macaques was higher than that in cynomolgus macaques. Introgressive hybridization with the Chinese rhesus macaque was supported in more than 80% (32/40) of cynomolgus macaques. CONCLUSIONS Chinese laboratory macaques had relatively low genetic diversity at the genomic level, and genetic differentiation in Chinese rhesus macaques was higher than in cynomolgus macaques. The genome of cynomolgus macaques has been shaped by introgression after hybridization with the Chinese rhesus macaques.
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Affiliation(s)
- Fangui Min
- Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Fengjiao Xu
- Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Shuwu Huang
- Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Ruike Wu
- Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Lan Zhang
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jing Wang
- Guangdong Laboratory, Animals Monitoring Institute, Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
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4
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Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome 2022; 33:91-99. [PMID: 34999909 PMCID: PMC8742695 DOI: 10.1007/s00335-021-09922-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022]
Abstract
Rhesus macaques (Macaca mulatta) are among the most extensively studied of nonhuman primates. This species has been the subject of many investigations concerning basic primate biology and behavior, including studies of social organization, developmental psychology, physiology, endocrinology, and neurodevelopment. Rhesus macaques are also critically important as a nonhuman primate model of human health and disease, including use in studies of infectious diseases, metabolic diseases, aging, and drug or alcohol abuse. Current research addressing fundamental biological and/or applied biomedical questions benefits from various genetic and genomic analyses. As a result, the genome of rhesus macaques has been the subject of more study than most nonhuman primates. This paper briefly discusses a number of information resources that can provide interested researchers with access to genetic and genomic data describing the content of the rhesus macaque genome, available information regarding genetic variation within the species, results from studies of gene expression, and other aspects of genomic analysis. Specific online databases are discussed, including the US National Center for Biotechnology Information, the University of California Santa Cruz genome browser, Ensembl genome browser, the Macaque Genotype and Phenotype database (mGAP), Rhesusbase, and others.
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5
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Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M. Comparison of sequencing data processing pipelines and application to underrepresented African human populations. BMC Bioinformatics 2021; 22:488. [PMID: 34627144 PMCID: PMC8502359 DOI: 10.1186/s12859-021-04407-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification. Results We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK “Best Practices” are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called. Conclusions We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04407-x.
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Affiliation(s)
- Gwenna Breton
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36, Uppsala, Sweden.
| | - Anna C V Johansson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Per Sjödin
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36, Uppsala, Sweden
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.,Science for Life Laboratory, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36, Uppsala, Sweden. .,Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. .,Science for Life Laboratory, Uppsala, Sweden.
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6
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Poirier C, Hamed SB, Garcia-Saldivar P, Kwok SC, Meguerditchian A, Merchant H, Rogers J, Wells S, Fox AS. Beyond MRI: on the scientific value of combining non-human primate neuroimaging with metadata. Neuroimage 2021; 228:117679. [PMID: 33359343 PMCID: PMC7903159 DOI: 10.1016/j.neuroimage.2020.117679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023] Open
Abstract
Sharing and pooling large amounts of non-human primate neuroimaging data offer new exciting opportunities to understand the primate brain. The potential of big data in non-human primate neuroimaging could however be tremendously enhanced by combining such neuroimaging data with other types of information. Here we describe metadata that have been identified as particularly valuable by the non-human primate neuroimaging community, including behavioural, genetic, physiological and phylogenetic data.
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Affiliation(s)
- Colline Poirier
- Biosciences Institute & Centre for Behaviour and Evolution, Faculty of Medical Sciences, Newcastle 6, UK.
| | - Suliann Ben Hamed
- Institut des Sciences Cognitives Marc Jeannerod, UMR 5229, Université de Lyon - CNRS, France
| | - Pamela Garcia-Saldivar
- Instituto de Neurobiología, UNAM, Campus Juriquilla. Boulevard Juriquilla No. 3001 Querétaro, Qro. 76230 México
| | - Sze Chai Kwok
- Shanghai Key Laboratory of Brain Functional Genomics, Key Laboratory of Brain Functional Genomics Ministry of Education, Shanghai Key Laboratory of Magnetic Resonance, Affiliated Mental Health Center (ECNU), Shanghai Changning Mental Health Center, School of Psychology and Cognitive Science, East China Normal University, Shanghai, China; Division of Natural and Applied Sciences, Duke Kunshan University, Duke Institute for Brain Sciences, Kunshan, Jiangsu, China; NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Adrien Meguerditchian
- Laboratoire de Psychologie Cognitive, UMR7290, Université Aix-Marseille/CNRS, Institut Language, Communication and the Brain 13331 Marseille, France
| | - Hugo Merchant
- Instituto de Neurobiología, UNAM, Campus Juriquilla. Boulevard Juriquilla No. 3001 Querétaro, Qro. 76230 México
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA 77030
| | - Sara Wells
- Centre for Macaques, MRC Harwell Institute, Porton Down, Salisbury, United Kingdom
| | - Andrew S Fox
- California National Primate Research Center, Department of Psychology, University of California, Davis, Davis, CA, 95616, USA
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7
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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8
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Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science 2021; 370:370/6523/eabc6617. [PMID: 33335035 DOI: 10.1126/science.abc6617] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022]
Abstract
The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.,Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marina Haukness
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jason Fernandes
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jessica M Storer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.,Institue for Systems Biology, Seattle, WA 98109, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth DeVogelaere
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Ludovica Mercuri
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | | | | | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Louis Picker
- Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA
| | - Ned H Kalin
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA
| | - Douglas Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jon Levine
- Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA
| | - David H Abbott
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
| | - Stanton B Gray
- The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA
| | - Mar M Sanchez
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
| | | | - Joseph W Kemnitz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.,Department of Ophthalmology and Vision Science, School of Medicine, University of California-Davis, Davis, CA 95817, USA
| | | | - Erin L Kinnally
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - John P Capitanio
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - J H Pate Skene
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mario Ventura
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Benedict Paten
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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9
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Infant inhibited temperament in primates predicts adult behavior, is heritable, and is associated with anxiety-relevant genetic variation. Mol Psychiatry 2021; 26:6609-6618. [PMID: 34035480 PMCID: PMC8613309 DOI: 10.1038/s41380-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/23/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
An anxious or inhibited temperament (IT) early in life is a major risk factor for the later development of stress-related psychopathology. Starting in infancy, nonhuman primates, like humans, begin to reveal their temperament when exposed to novel situations. Here, in Study 1 we demonstrate this infant IT predicts adult behavior. Specifically, in over 600 monkeys, we found that individuals scored as inhibited during infancy were more likely to refuse treats offered by potentially-threatening human experimenters as adults. In Study 2, using a sample of over 4000 monkeys from a large multi-generational family pedigree, we demonstrate that infant IT is partially heritable. The data revealed infant IT to reflect a co-inherited substrate that manifests across multiple latent variables. Finally, in Study 3 we performed whole-genome sequencing in 106 monkeys to identify IT-associated single-nucleotide variations (SNVs). Results demonstrated a genome-wide significant SNV near CTNNA2, suggesting a molecular target worthy of additional investigation. Moreover, we observed lower p values in genes implicated in human association studies of neuroticism and depression. Together, these data demonstrate the utility of our model of infant inhibited temperament in the rhesus monkey to facilitate discovery of genes that are relevant to the long-term inherited risk to develop anxiety and depressive disorders.
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10
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Buckley RM, Davis BW, Brashear WA, Farias FHG, Kuroki K, Graves T, Hillier LW, Kremitzki M, Li G, Middleton RP, Minx P, Tomlinson C, Lyons LA, Murphy WJ, Warren WC. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 2020; 16:e1008926. [PMID: 33090996 PMCID: PMC7581003 DOI: 10.1371/journal.pgen.1008926] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated cats with dwarfism and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models. The practice of genomic medicine is predicated on the availability of a high quality reference genome and an understanding of the impact of genome variation. Such resources have lead to countless discoveries in humans, however by working exclusively within the framework of human genetics, our potential for understanding diseases biology is limited, as similar analyses in other species have often lead to novel insights. The generation of Felis_catus_9.0, a new high quality reference genome for the domestic cat, helps facilitate the expansion of genomic medicine into the Felis lineage. Using Felis_catus_9.0 we analyze the landscape of genomic variation from a collection of 54 cats within the context of human gene constraint. The distribution of variant impacts in cats is correlated with patterns of gene constraint in humans, indicating the utility of this reference for identifying novel mutations that cause phenotypes relevant to human and cat health. Moreover, structural variant analysis revealed a novel variant for feline dwarfism in UGDH, a gene that has not been associated with dwarfism in any other species, suggesting a role for UGDH in cases of undiagnosed dwarfism in humans.
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Affiliation(s)
- Reuben M. Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Wesley A. Brashear
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Fabiana H. G. Farias
- Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics, Washington University, St. Louis, Missouri, United States of America
| | - Kei Kuroki
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Tina Graves
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - LaDeana W. Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | | | - Patrick Minx
- Donald Danforth Plant Science, St Louis, Missouri, United States of America
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Wesley C. Warren
- Division of Animal Sciences, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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11
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Oldt RF, Bussey KJ, Settles ML, Fass JN, Roberts JA, Reader JR, Komandoor S, Abrich VA, Kanthaswamy S. MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques ( Macaca mulatta). Comp Med 2020; 70:358-367. [PMID: 32753092 PMCID: PMC7574221 DOI: 10.30802/aalas-cm-19-000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 02/07/2020] [Indexed: 11/05/2022]
Abstract
In humans, abnormal thickening of the left ventricle of the heart clinically defines hypertrophic cardiomyopathy (HCM), a common inherited cardiovascular disorder that can precede a sudden cardiac death event. The wide range of clinical presentations in HCM obscures genetic variants that may influence an individual's susceptibility to sudden cardiac death. Although exon sequencing of major sarcomere genes can be used to detect high-impact causal mutations, this strategy is successful in only half of patient cases. The incidence of left ventricular hypertrophy (LVH) in a managed research colony of rhesus macaques provides an excellent comparative model in which to explore the genomic etiology of severe HCM and sudden cardiac death. Because no rhesus HCM-associated mutations have been reported, we used a next-generation genotyping assay that targets 7 sarcomeric rhesus genes within 63 genomic sites that are orthologous to human genomic regions known to harbor HCM disease variants. Amplicon sequencing was performed on 52 macaques with confirmed LVH and 42 unrelated, unaffected animals representing both the Indian and Chinese rhesus macaque subspecies. Bias-reduced logistic regression uncovered a risk haplotype in the rhesus MYBPC3 gene, which is frequently disrupted in both human and feline HCM; this haplotype implicates an intronic variant strongly associated with disease in either homozygous or carrier form. Our results highlight that leveraging evolutionary genomic data provides a unique, practical strategy for minimizing population bias in complex disease studies.
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Affiliation(s)
- Robert F Oldt
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona;,
| | - Kimberly J Bussey
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; BEYOND Center for Fundamental Concepts in Science, Arizona State University at the West Campus, Glendale, Arizona
| | - Matthew L Settles
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Joseph N Fass
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Jeffrey A Roberts
- California National Primate Research Center, University of California, Davis, California
| | - J Rachel Reader
- California National Primate Research Center, University of California, Davis, California
| | | | - Victor A Abrich
- Division of Cardiovascular Diseases, Mayo Clinic, Scottsdale, Arizona
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona; California National Primate Research Center, University of California, Davis, California
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12
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Lin Q, Lv JN, Wu KC, Zhang CJ, Liu Q, Jin ZB. Generation of Nonhuman Primate Model of Cone Dysfunction through In Situ AAV-Mediated CNGB3 Ablation. Mol Ther Methods Clin Dev 2020; 18:869-879. [PMID: 32953936 PMCID: PMC7479327 DOI: 10.1016/j.omtm.2020.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
A major challenge to the development of therapies for human retinal degenerative diseases is the lack of an ideal preclinical model because of the physiological differences between humans and most model animals. Despite the successful generation of a primate model through germline knockout of a disease-causing gene, the major issues restricting modeling in nonhuman primates (NHPs) are their relatively long lifespan, lengthy gestation, and dominant pattern of singleton births. Herein, we generated three cynomolgus macaques with macular in situ knockout by subretinal delivery of an adeno-associated virus (AAV)-mediated CRISPR-Cas9 system targeting CNGB3, the gene responsible for achromatopsia. The in vivo targeting efficiency of CRISPR-Cas9 was 12%-14%, as shown by both immunohistochemistry and single-cell transcriptomic analysis. Through clinical ophthalmic examinations, we observed a reduced response of electroretinogram in the central retina, which corresponds to a somatic disruption of CNGB3. In addition, we did not detect CRISPR-Cas9 residue in the heart, liver, spleen, kidney, brain, testis, or blood a year after administration. In conclusion, we successfully generated a NHP model of cone photoreceptor dysfunction in the central retina using an in situ CNGB3-knockout strategy.
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Affiliation(s)
- Qiang Lin
- Laboratory of Stem Cell & Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Ji-Neng Lv
- Laboratory of Stem Cell & Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Kun-Chao Wu
- Laboratory of Stem Cell & Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Chang-Jun Zhang
- Laboratory of Stem Cell & Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qin Liu
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Zi-Bing Jin
- Laboratory of Stem Cell & Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing 100730, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China
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13
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Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 2020; 16:e1008742. [PMID: 32392208 PMCID: PMC7241854 DOI: 10.1371/journal.pgen.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 05/21/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
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Affiliation(s)
- Marina Brasó-Vives
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Inna S. Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Diego A. Hartasánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Marcos Fernandez-Callejo
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Douglas L. Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Belen Lorente-Galdos
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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14
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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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15
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Martin ML, Bitzer AA, Schrader A, Bergmann-Leitner ES, Soto K, Zou X, Beck Z, Matyas GR, Dutta S. Comparison of immunogenicity and safety outcomes of a malaria vaccine FMP013/ALFQ in rhesus macaques (Macaca mulatta) of Indian and Chinese origin. Malar J 2019; 18:377. [PMID: 31775762 PMCID: PMC6880475 DOI: 10.1186/s12936-019-3014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
Background Indian-origin rhesus (InR) are preferred for research, but strict export restrictions continue to limit their use. Chinese-origin rhesus (ChR), although easier to procure, are genetically distinct from InR and differ in their immune response to infectious agents, such as the Simian Immunodeficiency Virus. The most advanced malaria vaccine, RTS,S (GlaxoSmithKline), is based on the circumsporozoite protein (CSP) of Plasmodium falciparum. The efficacy of RTS,S vaccine in the field remains low and short-lived; efforts are underway to improve CSP-based vaccines. Rhesus models can accelerate preclinical down-selection of the next generation of malaria vaccines. This study was used to determine if the safety and immunogenicity outcomes following vaccination with a CSP vaccine would differ in the InR and ChR models, given the genetic differences between the two sub-populations of rhesus. Methods The FMP013 vaccine, was composed of nearly full-length soluble P. falciparum CSP produced in Escherichia coli and was adjuvanted with the Army liposomal formulation (ALFQ). Three doses of the vaccine were administered in InR and ChR (n = 6) at 1-month intervals and the antibody and T cell responses were assessed. Results Local and systemic toxicity profile of FMP013 vaccine in InR and ChR were similar and they revealed that the FMP013 vaccine was safe and caused only mild and transient inflammatory adverse reactions. Following the first 2 vaccines, there was a slower acquisition of antibodies to the CSP repeat region in ChR. However after the 3rd vaccination the titers in the two models were comparable. The ChR group repeat-specific antibodies had higher avidity and ChR group showed higher inhibition of liver stage development activity compared to InR. There was no difference in T-cell responses to the FMP013 vaccine between the two models. Conclusions A difference in the quality of serological responses was detected between the two sub-populations of rhesus. However, both models confirmed that FMP013/ALFQ vaccine was safe, highly immunogenic, elicited functional antibodies and T-cell responses. Overall, the data suggests that rhesus of Indian and Chinese origins can be interchangeably used to compare the safety and immunogenicity of next-generation of malaria vaccines and adjuvants.
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Affiliation(s)
- Monica L Martin
- Division of Veterinary Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Alexis A Bitzer
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Andrew Schrader
- Division of Veterinary Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Elke S Bergmann-Leitner
- Immunology Core, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Kim Soto
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Xiaoyan Zou
- Malaria Department, Naval Medical Research Center, Silver Spring, MD, 20910, USA
| | - Zoltan Beck
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.,Henry M. Jackson Foundation, Rockville, MD, 20852, USA
| | - Gary R Matyas
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Sheetij Dutta
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
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16
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Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O'Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics 2019; 71:531-544. [PMID: 31321455 PMCID: PMC6790296 DOI: 10.1007/s00251-019-01125-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/02/2019] [Indexed: 02/03/2023]
Abstract
Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.
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Affiliation(s)
- John R Caskey
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Taylor Lee
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Robert J Maddox
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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17
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Ding Z, Ma M, Tao L, Peng Y, Han Y, Sun L, Dai X, Ji Z, Bai R, Jian M, Chen T, Luo L, Wang F, Bi Y, Liu A, Bao F. Rhesus Brain Transcriptomic Landscape in an ex vivo Model of the Interaction of Live Borrelia Burgdorferi With Frontal Cortex Tissue Explants. Front Neurosci 2019; 13:651. [PMID: 31316336 PMCID: PMC6610209 DOI: 10.3389/fnins.2019.00651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Lyme neuroborreliosis (LNB) is the most dangerous manifestation of Lyme disease caused by the spirochete Borrelia burgdorferi which can reach the central nervous system most commonly presenting with lymphocytic meningitis; however, the molecular basis for neuroborreliosis is still poorly understood. We incubated explants from the frontal cortex of three rhesus brains with medium alone or medium with added live Borrelia burgdorferi for 6, 12, and 24 h and isolated RNA from each group was used for RNA sequencing with further bioinformatic analysis. Transcriptomic differences between the ex vivo model of live Borrelia burgdorferi with rhesus frontal cortex tissue explants and the controls during the progression of the infection were identified. A total of 2249, 1064, and 420 genes were significantly altered, of which 80.7, 52.9, and 19.8% were upregulated and 19.3, 47.1, 80.2% were downregulated at 6, 12, and 24 h, respectively. Gene ontology and KEGG pathway analyses revealed various pathways related to immune and inflammatory responses during the spirochete infection were enriched which is suggested to have a causal role in the pathogenesis of neurological Lyme disease. Moreover, we propose that the overexpressed FOLR2 which was demonstrated by the real-time PCR and western blotting could play a key role in neuroinflammation of the neuroborreliosis based on PPI analysis for the first time. To our knowledge, this is the first study to provide comprehensive information regarding the transcriptomic signatures that occur in the frontal cortex of the brain upon exposure to Borrelia burgdorferi, and suggest that FOLR2 is a promising target that is associated with neuroinflammation and may represent a new diagnostic or therapeutic marker in LNB.
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Affiliation(s)
- Zhe Ding
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Mingbiao Ma
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lvyan Tao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Yun Peng
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Luyun Sun
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Xiting Dai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Zhenhua Ji
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Ruolan Bai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Miaomiao Jian
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Taigui Chen
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lisha Luo
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Feng Wang
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Yunfeng Bi
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Aihua Liu
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China.,Yunnan Province Integrative Innovation Center for Public Health, Diseases Prevention and Control, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
| | - Fukai Bao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,Yunnan Province Integrative Innovation Center for Public Health, Diseases Prevention and Control, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
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18
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Bimber BN, Yan MY, Peterson SM, Ferguson B. mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease. BMC Genomics 2019; 20:176. [PMID: 30841849 PMCID: PMC6402181 DOI: 10.1186/s12864-019-5559-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 02/22/2019] [Indexed: 11/17/2022] Open
Abstract
Background Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with parallel genetic risk alleles, underscores the value of macaques in the development of effective treatment strategies. Nonetheless, there are limited genomic resources available to support the exploration and discovery of macaque models of inherited disease. Notably, there are few public databases tailored to searching NHP sequence variants, and no other database making use of centralized variant calling, or providing genotype-level data and predicted pathogenic effects for each variant. Results The macaque Genotype And Phenotype (mGAP) resource is the first public website providing searchable, annotated macaque variant data. The mGAP resource includes a catalog of high confidence variants, derived from whole genome sequence (WGS). The current mGAP release at time of publication (1.7) contains 17,087,212 variants based on the sequence analysis of 293 rhesus macaques. A custom pipeline was developed to enable annotation of the macaque variants, leveraging human data sources that include regulatory elements (ENCODE, RegulomeDB), known disease- or phenotype-associated variants (GRASP), predicted impact (SIFT, PolyPhen2), and sequence conservation (Phylop, PhastCons). Currently mGAP includes 2767 variants that are identical to alleles listed in the human ClinVar database, of which 276 variants, spanning 258 genes, are identified as pathogenic. An additional 12,472 variants are predicted as high impact (SnpEff) and 13,129 are predicted as damaging (PolyPhen2). In total, these variants are predicted to be associated with more than 2000 human disease or phenotype entries reported in OMIM (Online Mendelian Inheritance in Man). Importantly, mGAP also provides genotype-level data for all subjects, allowing identification of specific individuals harboring alleles of interest. Conclusions The mGAP resource provides variant and genotype data from hundreds of rhesus macaques, processed in a consistent manner across all subjects (https://mgap.ohsu.edu). Together with the extensive variant annotations, mGAP presents unprecedented opportunity to investigate potential genetic associations with currently characterized disease models, and to uncover new macaque models based on parallels with human risk alleles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5559-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin N Bimber
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA.,Division of Pathobiology, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Melissa Y Yan
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Samuel M Peterson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA. .,Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA. .,Molecular and Medical Genetics Department, Oregon Health and Sciences University, Portland, OR, 97239, USA.
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19
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Veazey RS, Lackner AA. Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS. ILAR J 2018; 58:160-171. [PMID: 29228218 DOI: 10.1093/ilar/ilx032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/04/2017] [Indexed: 12/16/2022] Open
Abstract
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals. Research in NHP has led to "dogma changing" discoveries in immunology, infectious disease, and even our own genetics. We now know that many of our genes are retroviral remnants, or developed in response to archaic HIV-like retroviral infections. Early studies involving blood from HIV patients and in experiments in cultured tissues contributed to confusion regarding the cause of AIDS and impeded progress in the development of effective interventions. Research on the many retroviruses of different NHP species have broadened our understanding of human immunology and perhaps even our origins and evolution as a species. In combination with recent advances in molecular biology and computational analytics, research in NHPs has unique potential for discoveries that will directly lead to new cures for old human and animal diseases, including HIV/AIDS.
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Affiliation(s)
- Ronald S Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Andrew A Lackner
- Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Microbiology and Pathology and Laboratory Medicine, Tulane University School of Medicine
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20
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Comparative genome-wide survey of single nucleotide variation uncovers the genetic diversity and potential biomedical applications among six Macaca species. Int J Mol Sci 2018; 19:ijms19103123. [PMID: 30314376 PMCID: PMC6212917 DOI: 10.3390/ijms19103123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/21/2018] [Accepted: 10/08/2018] [Indexed: 12/30/2022] Open
Abstract
Macaca is of great importance in evolutionary and biomedical research. Aiming at elucidating genetic diversity patterns and potential biomedical applications of macaques, we characterized single nucleotide variations (SNVs) of six Macaca species based on the reference genome of Macaca mulatta. Using eight whole-genome sequences, representing the most comprehensive genomic SNV study in Macaca to date, we focused on discovery and comparison of nonsynonymous SNVs (nsSNVs) with bioinformatic tools. We observed that SNV distribution patterns were generally congruent among the eight individuals. Outlier tests of nsSNV distribution patterns detected 319 bins with significantly distinct genetic divergence among macaques, including differences in genes associated with taste transduction, homologous recombination, and fat and protein digestion. Genes with specific nsSNVs in various macaques were differentially enriched for metabolism pathways, such as glycolysis, protein digestion and absorption. On average, 24.95% and 11.67% specific nsSNVs were putatively deleterious according to PolyPhen2 and SIFT4G, respectively, among which the shared deleterious SNVs were located in 564–1981 genes. These genes displayed enrichment signals in the ‘obesity-related traits’ disease category for all surveyed macaques, confirming that they were suitable models for obesity related studies. Additional enriched disease categories were observed in some macaques, exhibiting promising potential for biomedical application. Positively selected genes identified by PAML in most tested Macaca species played roles in immune and nervous system, growth and development, and fat metabolism. We propose that metabolism and body size play important roles in the evolutionary adaptation of macaques.
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21
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Harding JD. Nonhuman Primates and Translational Research: Progress, Opportunities, and Challenges. ILAR J 2017; 58:141-150. [PMID: 29253273 PMCID: PMC5886318 DOI: 10.1093/ilar/ilx033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 01/15/2023] Open
Abstract
Nonhuman primates (NHPs) are the closest animal models to humans regarding genetics, physiology and behavior. Therefore, NHPs are usually a critical component in translational research projects aimed at developing therapeutics, vaccines, devices or other interventions aimed at preventing, curing or ameliorating human disease. NHPs are often used in conjunction with other animal models, such as rodents, and results obtained using NHPs must often be used as the final criterion for establishing the potential efficacy of a pharmaceutical or vaccine before transition to human clinical trails. In some cases, NHPs may be the only relevant animal models for a particlular translational study. This issue of the ILAR journal brings together, in one place, articles that discuss the use of NHP models for studying human diseases that are highly prevalent and that cause extraordinary human suffering and financial and social burdens. Topics covered in detail include: tuberculosis; viral hepatitis; HIV/AIDS; neurodegenerative disorders; Substance abuse disorders; vision and prevention of blindness; disorder associated with psychosocial processes, such as anxiety, depression and loneliness; cardiovascular disease; metabolic disease, such as obesity and metabolic syndrome; respiratory disease; and female reproduction, prenatal development and women's health. Proper husbandry of NHPs that reduces stress and maintains animal health is critical for the development of NHP models. This issue of the journal includes a review of procedures for environmental enrichment, which helps assure animal health and wellbeing. Taken together, these articles provide detailed reviews of the use of NHP models for translational investigations and discuss successes, limitations, challenges and opportunities associated with this research.
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Affiliation(s)
- John D Harding
- John D. Harding, PhD, recently retired after several years of service at the National Institutes of Health in Bethesda, Maryland, where he was program officer for grants funding the US National Primate Research Centers.
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